Background: Methotrexate (MTX), is a folate antagonist that inhibits cell development and is used to treat a wide range of disorders. The goal of the current study was to investigate the toxic effect of MTX on the bone, heart and kidney of albino rat foetuses. Methods: Thirty-five rats were divided into 5 groups, MTX was given orally (0.03 mg/kg) for 10 days to G1 & G2 (males and females) and before being allowed to mate with the control group (females and males respectively). G3 (males and females) was given orally (0.03 mg/kg) for 10 days before being allowed to mate with each other. G4 pregnant females were given (0.03mg/kg) of MTX orally every day from the 1^st to the 20^th day of pregnancy. Results: The changes suggested that MTX treatment caused developmental abnormalities including partial ossification of some skull bones, and vertebrae of limbs, and a notable decrease in the length of most long bones in both limbs. The kidney of MTX-treated groups showed changes such as capsular dilatation, renal corpuscle distortion, shrunken glomeruli, edoema, and necrosis in renal tubules of the renal medulla. It also induced histopathological changes in cardiac muscle tissue, including widely distributed vacuolated spaces, congested blood vessels, leukocytic infiltration, cardiomyocyte disarrangement with pyknotic nuclei, necrosis and a lack of regular arrangement.