The methanol root extracts of Carica papaya (Pawpaw) are used in eastern Nigeria for the treatment of malaria, hepatitis and jaundice. The aim of this study was to investigate the effects of the fractions isolated from C. papaya methanol root extract on fertility in male Wistar rats using sperm counts, percentage defective sperm cells (morphology), biochemical and hormonal assays as biomarkers. The roots of C. papaya were extracted using 80% methanol for 72 h. Oral acute toxicity study was done with the crude extract for 24 h. The extract was fractionated by column chromatography using petroleum ether, chloroform, ethyl acetate and methanol. The petroleum ether fraction was further fractionated on preparative TLC using ethyl acetate-methanol solvent systems to isolate CPFE 1, CPFE 2 and CPFM 1. The 3 fractions (75 mg/kg) were used to treat male Wistar rats orally for 60 days. Animals were euthanized and testes collected, homogenized and used for sperm count and motility. Plasma and serum were used to assay biochemical parameters including aspartate aminotransferase (AST), blood urea nitrogen (BUN), total bilirubin (TB), alkaline phosphatase (ALP), alanine aminotransferase (ALT), gamma glutamyl transferase (GGT), triglycerides, hormones (LH and FSH). Histopathological study of the testes, kidney, heart and liver were conducted. Acute toxicity result showed that C. papaya root extract produced no mortalities at the dose of 2000 mg/kg but induced CNS-related symptoms as well as diuresis. The fractions significantly (P < 0.01) produced decreases in sperm counts and increased the percentage of defective sperm cells. There were significant (P < 0.05) increases in aspartate aminotransferase (AST) and blood urea nitrogen (BUN). Histopathological studies showed mild kidney and cardiac hyperaemia, slight