In-transit melanoma is characterized by an aggressive pattern of recurrence that is associated with a poorer prognosis. Because in-transit melanoma is considered to result from the intralymphatic trapping of melanoma cells between the primary tumor and regional lymph nodes, it provides an excellent model to assess genetic events associated with early metastasis. The hypothesis of this study was to determine whether in-transit metastases are clonal in origin and therefore, may have specific genetic alterations uniquely associated with this disease and the development of early metastasis. This was assessed using loss of heterozygosity (LOH) analysis for specific DNA microsatellite loci. Seventy-nine paraffin-embedded in-transit melanoma lesions from 25 patients (range, 2 to 9 lesions per patient; average, 3.4 lesions per patient) were assessed for LOH using eight microsatellite DNA markers on six chromosomes. In 19 of 25 patients (76%) LOH was demonstrated for at least one marker. The most frequent microsatellite marker demonstrating LOH was D9S157 (56%). Using LOH microsatellite markers to assess intertumor heterogeneity, six of 79 tumors (7.6%) demonstrated different profiles when compared to other lesions from the same patient. In-transit metastases from those patients demonstrating intertumor heterogeneity were further assessed using laser capture microdissection and DNA analysis, and revealed no significant intratumor heterogeneity. In conclusion, LOH was frequently observed in in-transit melanoma metastasis. Based on LOH analysis, in-transit metastases are clonal in origin. The establishment of clinically successful in-transit melanoma metastasis requires specific genetic events that seem to be unique and homogeneous for each patient.