The diagnosis of condyloma acuminatum generally relies on the presence of characteristic clinical features. However, atypical cases can cause diagnostic problems. With the development of the molecular biological techniques, the disease can be readily diagnosed. A case of atypical condyloma acuminatum in a 25-year-old male is reported, he presented with midpenile hypospadias and a mass extending from the scrotum to the corona through the chordee deformity. The clinical diagnosis was condyloma acuminatum. A tissue specimen was obtained for histopathological analysis and in-situ hybridization assay for human papilloma virus. Histopathological analysis showed papilloma. The immunohistochemical assay was negative for human papilloma virus. However, in-situ hybridization for human papilloma virus was strongly positive. Condyloma acuminatum should be suspected in hypospadias patients with atypical papillomatous lesions on the chordee deformity. In-situ hybridization is extremely useful in establishing the diagnosis. Since condyloma acuminatum is the cause of viral contamination and malignant transformation, it is worth considering histopathological examination and molecular biological techniques to protect both the patient and the sexual partner.