Introduction: Early detection of acute Hepatitis A virus infection (HAV) allows adopting proper treatment measures, rapid recovery, and avoiding side effects. This study compares PCR assay with serology for diagnosing acute HAV infection. Methods: Twenty samples from patients presenting clinical symptoms of acute hepatitis were tested for anti-HAV IgM antibodies. Genomic RNA was extracted from IgM-positive samples, cDNA was synthesized and examined for genomic HAV using a specific HAV real-time detection kit and a nested PCR. Results: Among 20 sera, 14 were positive for anti-HAV IgM antibodies. The specific real-time PCR and nested PCR showed agreement, and both detected HAV genetic material in 3 out of 14 samples. Conclusion: High levels of anti-HAV IgM antibodies do not necessarily indicate acute HAV infection in people presenting clinical symptoms of the disease. Measuring IgM antibody levels alongside molecular detection of virus genome by DNA-based methods assay can lead to an accurate, timely, and reliable diagnosis of active HAV infection.