Quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) for specific melanoma markers is more sensitive than histology for detecting cells of melanocytic origin in sentinel lymph nodes (SLNs) in cutaneous melanoma. The clinical significance of a positive qRT-PCR analysis is unclear. We performed qRT-PCR for the presence of MART-1 and tyrosinase in SLNs from 93 melanoma patients, and then followed these patients clinically (median follow-up time 43.5 months). We found a significant correlation between disease progression and presence of MART-1 mRNA in SLNs (p=0.02), but no correlation with the amount of MART-1 mRNA as measured by qRT-PCR. No correlation between histology and recurrence was detected, recurrence rates being low in both histology-negative (12%) and -positive (15%) patients. We found a significant difference in disease recurrence between patients positive by both histology and RT-PCR and patients negative by both methods (15% vs 0%, p=0.02). However, a significant difference in disease recurrence was also found when comparing patients negative by both methods with patients positive by RT-PCR but negative by histology (0% vs 19%, p=0.009). This suggests that the presence of submicroscopic metastases may influence prognosis, indicating that RT-PCR detection of melanocytic cells in SLNs may be an important diagnostic marker.