RMS can occur in almost any soft-tissue site in the body; the most common primary sites are genitourinary (24%), parameningeal (16%), extremity (19%), orbit (9%), other head and neck (10%), and miscellaneous other sites (22%). RMS often presents as a mass, but signs and symptoms can vary widely depending on the site of the primary tumor. Genitourinary tumors may present with hematuria, urinary tract obstruction, and/or a scrotal or vaginal mass. Tumors that arise in the retroperitoneum and mediastinum can become quite large before producing signs and symptoms. Parameningeal tumors may present with cranial nerve dysfunction, symptoms of sinusitis, ear discharge, headaches, and facial pain. Orbital tumors often present with orbital swelling and proptosis. Extremity tumors generally present as a rapidly enlarging, firm mass in the relevant tissue. The cancer's prevalence in the head, face, and neck will often allow for earlier signs of the disease simply due to the obvious nature of tumors in these locations. Despite the varying presentation and typically aggressive nature of the disease, RMS has the potential to be diagnosed and treated early. The fourth IRSG study found that 23% of patients were diagnosed in time for a complete resection of their cancer, and 15% had resection with only minimal remnants of the diseased cells.

Given the difficulty in diagnosing rhabdomyosarcoma, definitive classification of subsets has proven difficult. As a result, classification systems vary by institute and organization. However, rhabdomyosarcoma can be generally divided into three histological subsets:

- "Embryonal rhabdomyosarcoma" (ERMS) is the most common histological variant, comprising approximately 60–70% of childhood cases. It is most common in children 0–4 years old, with a maximum reported incidence of 4 cases per 1 million children. ERMS is characterized by spindle-shaped cells with a stromal-rich appearance, and the morphology is similar to the developing muscle cells of a 6–8 week old embryo. Tumors often present in the head and neck as well as the genitourinary tract. ERMS also has two defined subtypes, botryoid and spindle cell ERMS, and these subtypes are associated with a favorable prognosis.

- Subtypes of ERMS

- Botryoid ERMS is almost always found in mucosal lined organs including the vagina, bladder, and nasopharynx (although presentation in the nasopharynx typically affects older children). It often presents in patients <1 year old as a round, grape-like mass on the affected organ. Histologically, cells of the botryoid variant are defined by a dense tumor layer under an epithelium (cambium layer).

- Spindle cell rhabdomyosarcoma comprises about 3% of all RMS cases. This subtype is very similar to that of leiomyosarcoma (cancer of the smooth muscle tissue), and it has a fascicular, spindled, and leiomyomatous growth pattern with notable rhabdomyoblastic differentiation . It occurs most commonly in the paratesticular region, and the prognosis for this particular form of RMS is excellent with a reported 5 year survival rate of 95%.

- "Alveolar rhabdomyosarcoma" (ARMS) is the second most common type. ARMS comprises approximately 20–25% of RMS-related tumors, and it is equally distributed among all age groups with an incidence of about 1 case per 1 million people ages 0 to 19. For this reason, it is the most common form of RMS observed in young adults and teenagers, who are less prone to the embryonal variant. This type of RMS is characterized by densely-packed, round cells that arrange around spaces similar in shape to pulmonary alveoli, although variants have been discovered without these characteristic alveolar spacings. ARMS tends to form more often in the extremities, trunk, and peritoneum. It is also typically more aggressive than ERMS.

- "Anaplastic (undifferentiated) rhabdomyosarcoma", also known as "pleomorphic rhabdomyosarcoma", is the final variant of RMS recognized in most classification systems. Anaplastic rhabdomyosarcoma is defined by the presence of anaplastic cells with large, lobate hyperchromatic nuclei and multipolar mitotic figures. These tumors display high heterogeneity and extremely poor differentiation. The anaplastic cells may be diffuse or localized, with the diffuse variation correlating to a worse prognosis. It occurs most often in adults, rarely in children, and is often discovered in the extremities. Due to the lack of discernible separation among cancers of this type, clinicians will often label undiagnosed sarcomas with little to no discernible features as anaplastic RMS. It is the most aggressive type of RMS, and will often require intensive treatment.

There is also an extremely rare subtype of RMS that has been described as "sclerosing rhabdomyosarcoma" by "Folpe, et al", but it is not a currently recognized subtype by the NCI or WHO. This subtype has characteristic histology involving hyaline sclerosis and pseudovascular development. Its origins are unclear, but some studies have pointed to an association with embryonal RMS.

Multiple classification systems have been proposed for guiding management and treatment, and the most recent and widely used classification system is the "International Classification of Rhabdomyosarcoma" or ICR. It was created by the IRSG in 1995 after their series of four multi-institutional trials aimed at studying the presentation, histology, epidemiology, and treatment of RMS (IRSG I–IV). The ICR system is based on prognostic indicators identified in IRSG I–IV. Pleomorphic rhabdomyosarcoma usually occurs in adults rather than children, and is therefor not included in this system. Sclerosing rhabdomyosarcoma is also not included in this system due to its rare presentation and weak classification schema.

Ewing's sarcoma is more common in males (1.6 male:1 female) and usually presents in childhood or early adulthood, with a peak between 10 and 20 years of age. It can occur anywhere in the body, but most commonly in the pelvis and proximal long tubular bones, especially around the growth plates. The diaphyses of the femur are the most common sites, followed by the tibia and the humerus. Thirty percent are overtly metastatic at presentation. Patients usually experience extreme bone pain.

Signs and symptoms include: intermittent fevers, anemia, leukocytosis, increased sedimentation rate, and other symptoms of inflammatory systemic illness. Also, depending on the type, progression, and location of the tumor, great pain may occur.

According to the Bone Cancer Research Trust (BCRT), the most common symptoms are: localized pain, swelling, and sporadic bone pain with variable intensity. The swelling is most likely to be visible if the sarcoma is located on a bone near the surface of the body, but when it occurs in other places deeper in the body, like on the pelvis, it may not be visible.

The prognosis for rhabdomyosarcoma has improved greatly in recent decades, with over 70% of patients surviving for five years after diagnosis.

Spindle cell rhabdomyosarcoma is a subtype of embryonal rhabdomyosarcoma first described by Cavazzana, Schmidt and Ninfo in 1992. This subtype has a more favorable clinical course and prognosis than usual embryonal rhabdomyosarcoma. Spindle cell rhabdomyosarcoma typically occurs in young males and most commonly occurs in paratesticular soft tissue, followed by the head and neck.

ERMS is the more common of two major subtypes of rhabdomyosarcoma, the other being alveolar rhabdomyosarcoma.

It has been informally classified as a "small round blue cell tumor" because of the characteristic microscopic appearance of its cells after histological staining with hematoxylin and eosin.

Malignant rhabdoid tumour (MRT) is a very aggressive form of tumour originally described as a variant of Wilms' tumour, which is primarily a kidney tumour that occurs mainly in children.

MRT was first described as a variant of Wilms' tumour of the kidney in 1978. MRTs are a rare and highly malignant childhood neoplasm. Later rhabdoid tumours outside the kidney were reported in many tissues including the liver, soft tissue, and the central nervous system. Several cases of primary intracranial MRT have been reported since its recognition as a separate entity in 1978. The term "rhabdoid" was used due to its similarity with rhabdomyosarcoma under the light microscope. The exact pathogenesis of MRT is unknown.

The cerebellum is the most common location for primary intracerebral MRT (i.e., AT/RT). Biggs et al. were first to report a primary intracranial MRT around 1987.

Although the cell of origin is not known, cytogenetic studies have suggested a common genetic basis for rhabdoid tumours regardless of location with abnormalities in chromosome 22 commonly occurring.

Ewing sarcoma or Ewing's sarcoma () is a malignant small, round, blue cell tumor. It is a rare disease in which cancer cells are found in the bone or in soft tissue. The most common areas in which it occurs are the pelvis, the femur, the humerus, the ribs and clavicle (collar bone).

Since a common genetic locus is responsible for a large percentage of Ewing sarcoma and primitive neuroectodermal tumors, these are sometimes grouped together in a category known as the Ewing family of tumors.

Ewing sarcoma occurs most frequently in teenagers and young adults, with a male/female ratio of 1.6:1.

Although usually classified as a bone tumor, Ewing's sarcoma can have characteristics of both mesodermal and ectodermal origin, making it difficult to classify.

James Ewing (1866–1943) first described the tumour, establishing that the disease was separate from lymphoma and other types of cancer known at that time.

Endodermal sinus tumor (EST), also known as yolk sac tumor (YST), is a member of the germ cell tumor group of cancers. It is the most common testicular tumor in children under 3, and is also known as infantile embryonal carcinoma. This age group has a very good prognosis. In contrast to the pure form typical of infants, adult endodermal sinus tumors are often found in combination with other kinds of germ cell tumor, particularly teratoma and embryonal carcinoma. While pure teratoma is usually benign, endodermal sinus tumor is malignant.

Considerable debate has been focused on whether AT/RTs are the same as rhabdoid tumours of the kidney (i.e., just extra-renal MRTs (malignant rhabdoid tumours)). The recent recognition that both CNS atypical teratoid/rhabdoid tumours (AT/RTs) and MRTs have deletions of the INI1 gene in chromosome 22 indicates that rhabdoid tumours of the kidney and brain are identical or closely related entities, although the CNS variant tends to have its mutations on Taxon 9 and MRTs elsewhere. This observation is not surprising because rhabdoid tumours at both locations possess similar histologic, clinical, and demographic features. Moreover, 10-15% of patients with MRTs have synchronous or metachronous brain tumours, many of which are second primary malignant rhabdoid tumours. This similarity excludes composite rhabdoid tumours, which occur mainly in adults.

Alveolar rhabdomyosarcoma (ARMS) is a sub-type of the rhabdomyosarcoma soft tissue cancer family whose lineage is from mesenchymal cells and are related to skeletal muscle cells. ARMS tumors resemble the alveoli tissue that can be found in the lungs. Tumor location varies from patient to patient, but is commonly found in the head and neck region, male and female urogenital tracts, the torso, and extremities. Two fusion proteins can be associated with ARMS, but are not necessary, PAX3-FKHR (now known as FOXO1). and PAX7-FKHR. In children and adolescents ARMS accounts for about 1 percent of all malignancies, has an incidence rate of 1 per million, and most cases occur sporadically with no genetic predisposition.

In the United States, about 20-30 cases are reported each year. This may be a gross underestimate of the total number of cases as few laboratories have the reagents and expertise to make the diagnosis. The symptoms are similar to other forms of cancer and dependent on the stage. While generalized symptoms (weight loss and fatigue) may be seen, site specific symptoms are also present. If the tumor involves the head and neck region (in about 35%), then pain, a mass, obstructive symptoms, among others, may be experienced. NUT midline carcinomas are not specific to any tissue type or organ.

Common sites include the head, neck and mediastinum. The median age at diagnosis is 17 years, but older patients may be affected.

AT/RT may be related to malignant rhabdoid tumor (MRT), which occurs outside the CNS, usually in the kidney. The finding that AT/RT and MRT both have deletions of the "INI1" gene indicates that rhabdoid tumors of the kidney and brain are at least closely related. AT/RT and MRT also have similar histology and similar clinical and demographic features. Moreover, 10–15% of MRT patients have simultaneous or subsequent brain tumors, many of which are secondary or primary MRT.

Signs and symptoms are mainly due to secondary increased intracranial pressure due to blockage of the fourth ventricle and are usually present for 1 to 5 months before diagnosis is made. The child typically becomes listless, with repeated episodes of vomiting, and a morning headache, which may lead to a misdiagnosis of gastrointestinal disease or migraine. Soon after, the child will develop a stumbling gait, truncal ataxia, frequent falls, diplopia, papilledema, and sixth cranial nerve palsy. Positional dizziness and nystagmus are also frequent, and facial sensory loss or motor weakness may be present. Decerebrate attacks appear late in the disease.

Extraneural metastasis to the rest of the body is rare, and when it occurs, it is in the setting of relapse, more commonly in the era prior to routine chemotherapy.

It is classified into two types, based on location in the body: peripheral PNET and CNS PNET.

The histology of EST is variable, but usually includes malignant endodermal cells. These cells secrete alpha-fetoprotein (AFP), which can be detected in tumor tissue, serum, cerebrospinal fluid, urine and, in the rare case of fetal EST, in amniotic fluid. When there is incongruence between biopsy and AFP test results for EST, the result indicating presence of EST dictates treatment. This is because EST often occurs as small "malignant foci" within a larger tumor, usually teratoma, and biopsy is a sampling method; biopsy of the tumor may reveal only teratoma, whereas elevated AFP reveals that EST is also present. GATA-4, a transcription factor, also may be useful in the diagnosis of EST.

Diagnosis of EST in pregnant women and in infants is complicated by the extremely high levels of AFP in those two groups. Tumor surveillance by monitoring AFP requires accurate correction for gestational age in pregnant women, and age in infants. In pregnant women, this can be achieved simply by testing maternal serum AFP rather than tumor marker AFP. In infants, the tumor marker test is used, but must be interpreted using a reference table or graph of normal AFP in infants.

Primitive neuroectodermal tumor (PNET) is a malignant (cancerous) neural crest tumor. It is a rare tumor, usually occurring in children and young adults under 25 years of age. The overall 5 year survival rate is about 53%.

It gets its name because the majority of the cells in the tumor are derived from neuroectoderm, but have not developed and differentiated in the way a normal neuron would, and so the cells appear "primitive".

PNET belongs to the Ewing family of tumors.

Medulloepithelioma most commonly affect children between 6 months and 5 years; rarely, this tumour may occur congenitally or beyond this age range. Incidence is equal in males and females.

Clinical signs and symptoms depend on the location of the tumor.

Since many of the tumors occur in the posterior fossa, they present like other posterior fossa tumors, often with headache, vomiting, lethargy, and ataxia (unsteady gait). A case of a seven-month-old child with a primarily spinal tumor that presented with progressive paraplegia and abnormal feeling in the legs was reported.

There are few early warning signs that a patient has a DSRCT. Patients are often young and healthy as the tumors grow and spread uninhibited within the abdominal cavity. These are rare tumors and symptoms are often misdiagnosed by physicians. The abdominal masses can grow to enormous size before being noticed by the patient. The tumors can be felt as hard, round masses by palpating the abdomen.

First symptoms of the disease often include abdominal distention, abdominal mass, abdominal or back pain, gastrointestinal obstruction, lack of appetite, ascites, anemia, and/or cachexia.

Other reported symptoms include unknown lumps, thyroid conditions, hormonal conditions, blood clotting, kidney or urological problems, testicle, breast, uterine, vaginal, or ovarian masses.

Medulloepithelioma is a rare, primitive, fast-growing brain tumour thought to stem from cells of the embryonic medullary cavity. Tumours originating in the ciliary body of the eye are referred to as embryonal medulloepitheliomas, or diktyomas.

A highly malignant undifferentiated primitive neuroepithelial tumour of children, medulloepithelioma may contain bone, cartilage, skeletal muscle, and tends to metastasize extracranially.

NUT carcinoma (formerly NUT midline carcinoma), is a rare genetically defined, very aggressive squamous cell epithelial cancer that usually arises in the midline of the body and is characterized by a chromosomal rearrangement in the nuclear protein in testis gene. In approximately 75% of cases, the coding sequence of "NUTM1" on chromosome 15q14 is fused to "BRD4" or "BRD3", which creates a chimeric gene that encodes the "BRD-NUT" fusion protein. The remaining cases, the fusion of NUTM1 is to an unknown partner gene, usually called "NUT"-variant.

Childhood rhabdomyosarcoma consists of three subgroups. Embryonal is the most common among children and young adults. Alveolar and anaplastic rhabdomyosarcoma occur in the teenage years.

- Embryonal rhabdomyosarcoma develops within the first seven weeks of the embryo's development. Rapid cell growth causes masses to form along the head, neck, urinary tract, and genital organs.

- Alveolar, the second most common group, is seen later in life. During the teen years, large muscle groups come under attack, including the torso and large appendages. Aggressive treatment is needed to stop or limit progression of alveolar rhabdomyosarcoma.

- Anaplastic rhabdomyosarcoma is rarely seen in children and only precise intensive lab work can identify it.

The first symptoms of neuroblastoma are often vague making diagnosis difficult. Fatigue, loss of appetite, fever, and joint pain are common. Symptoms depend on primary tumor locations and metastases if present:

- In the abdomen, a tumor may cause a swollen belly and constipation.

- A tumor in the chest may cause breathing problems.

- A tumor pressing on the spinal cord may cause weakness and thus an inability to stand, crawl, or walk.

- Bone lesions in the legs and hips may cause pain and limping.

- A tumor in the bones around the eyes or orbits may cause distinct bruising and swelling.

- Infiltration of the bone marrow may cause pallor from anemia.

Neuroblastoma often spreads to other parts of the body before any symptoms are apparent and 50 to 60% of all neuroblastoma cases present with metastases.

The most common location for neuroblastoma to originate (i.e., the primary tumor) is in the adrenal glands. This occurs in 40% of localized tumors and in 60% of cases of widespread disease. Neuroblastoma can also develop anywhere along the sympathetic nervous system chain from the neck to the pelvis. Frequencies in different locations include: neck (1%), chest (19%), abdomen (30% non-adrenal), or pelvis (1%). In rare cases, no primary tumor can be discerned.

Rare but characteristic presentations include transverse myelopathy (tumor spinal cord compression, 5% of cases), treatment-resistant diarrhea (tumor vasoactive intestinal peptide secretion, 4% of cases), Horner's syndrome (cervical tumor, 2.4% of cases), opsoclonus myoclonus syndrome and ataxia (suspected paraneoplastic cause, 1.3% of cases), and hypertension (catecholamine secretion or renal artery compression, 1.3% of cases).

Childhood rhabdomyosarcoma is difficult to diagnose. Factors that increase the likelihood of this cancer include Li-Fraumeni syndrome, type one Neurofibromatosis, Beckwith-Wiedemann syndrome, Costello syndrome, and Noonan syndrome. Each contribute to deformations of bones, tissue, and muscles.