The results indicated that ITPA 94C>A was significantly associated with 6-MP-induced neutropenia (OR 2.38, 95% CI: 1.56–3.62; p = 0.005) and hepatotoxicity (OR 1.98, 95% CI: 1.32–2.95; p = 0.0009); however, no significant association was found between the ITPA 94C>A variant and 6-MP-induced leukopenia (OR 1.75, 95% CI: 0.74–4.12; p = 0.20). Here, ITPA is linked to Decreased total neutrophil count.