Circadian rhythms are influenced by the expression of clock genes, which are controlled by a feedback mechanism that allows a rhythmic variation during 24 hours. Aberrant expression of clock genes has been previously observed in melanoma. The largest of circadian genes, Neuronal PAS domain protein 2 (NPAS2), encodes for a member of the basic helix-loop-helix--PAS class of transcription factors and is expressed in the forebrain and in some peripheral organs such as liver and skin. It has been previously proven that NPAS2 is involved in cell proliferation, DNA damage repair and malignant transformation as a tumour suppressor. Therefore, in this study we investigated the correlation between the NPAS2 gene nonsynonymous polymorphism (Ala394Thr ; rs2305160) and the risk of melanoma. Study included 294 melanoma patients (143 males and 151 females) and 356 healthy control subjects (271 males and 85 females). Genotyping of Ala394Thr gene polymorphism was performed with TaqMan Pre-designed SNP Genotyping Assay. Our results demonstrate a statistically significant difference in both genotype and allele frequencies in female patients compared with female control subjects (p = 0.02 and p = 0.004, respectively), showing that A/A genotype, as well as A allele, could be one of the risk factors for developing melanoma. Moreover, the significant difference was observed in all inheritance models that include A/A genotype in female subjects. Obtained results suggest that the A/A genotype could be one of the risk factors for developing melanoma in females.