Objective Men with the metabolic syndrome (MetS) have low plasma testosterone (T) levels. The aim of this study was to establish whether the normalization of plasma T improves the features of the MetS. Design A randomized, placebo‐controlled, double‐blinded, phase III trial of 184 men suffering from both the MetS and hypogonadism. Patients One hundred and eighty‐four men, aged 35–70, with the MetS and hypogonadism (baseline total T level <12·0 nm or calculated free T level <225 pm.), recruited in the outpatient andrology and urology clinic, Research Center for Endocrinology in Moscow, Russia. Intervention Treatment for 30 weeks with either parenteral T undecanoate (n = 113; TU; 1000 mg IM) or placebo (n = 71), administered at baseline, and after 6 and 18 weeks. One hundred and five (92·9%) men receiving TU and 65 (91·5%) receiving placebo completed the trial. Measurements Body weight, body mass index (BMI), waist circumference (WC), hip circumference, waist‐to‐hip ratio, insulin, leptin, glucose, cholesterol, triglycerides, high‐density lipoprotein cholesterol, low‐density lipoprotein cholesterol, C‐reactive protein (CRP), interleukin‐1‐beta (IL‐1β), interleukin‐6 (IL‐6), interleukin‐10 (IL‐10) and tumour necrosis factor‐alpha (TNF‐α). Results There were significant decreases in weight, BMI and WC in the TU vs placebo group. Levels of leptin and insulin also decreased, but there were no changes in serum glucose or lipid profile. Of the inflammatory markers, IL‐1β, TNF‐α and CRP decreased, while IL‐6 and IL‐10 did not change significantly. Conclusions Thirty weeks of T administration normalizing plasma T in hypogonadal men with the MetS improved some components of the MetS and a number of inflammatory markers.