The aim of the present study was to evaluate the prevalence of vitamin B12 (B12) deficiency in kidney transplant recipients (KTR) and its possible association with B12 dietary intake, body adiposity and immunosuppressive drugs. In this cross-sectional study, we included 225 KTR, aged 47·50 (sd 12·11) years, and 125 (56 %) were men. Serum levels of B12 were determined by chemiluminescent microparticle intrinsic factor assay and the cut-off of 200 pg/ml was used to stratify KTR into B12-sufficient or B12-deficient group. B12 dietary intake was evaluated by three 24 h dietary recalls and was considered adequate when ≥2·4 μg/d. Body adiposity was estimated after taking anthropometric measures and using the dual-energy X-ray absorptiometry (DXA) method. B12 deficiency was seen in 14 % of the individuals. B12-deficient group, compared with the B12-sufficient group, exhibited lower intake of B12 (median 2·42 (interquartile range (IQR) 1·41–3·23) v. 3·16 (IQR 1·94–4·55) μg/d, P = 0·04) and higher values of waist circumference (median 96·0 (IQR 88·0–102·5) v. 90·0 (IQR 82·0–100·0) cm, P = 0·04). When the analysis included only women, B12 deficiency was associated with higher total and central body adiposity measurements obtained with anthropometry (BMI, body adiposity index, waist and neck circumferences) and DXA (total and trunk body fat). Among individuals with adequate intake of B12, the deficiency of this vitamin was more frequently seen in those using mycophenolate mofetil (MMF) (17 %) v. azathioprine (2 %), P = 0·01. In conclusion, the prevalence of B12 deficiency in KTR was estimated as 14 % and was associated with reduced intake of B12 as well as higher adiposity, especially in women, and with the use of MMF.