Digito-rectal examination (DRE) of the prostate provides useful information on the state of prostate growth and on the presence of suspected peripheral nodules. The aim of this study is to describe the clinical and biochemical correlates of finding an enlarged prostate size at DRE in subjects with sexual dysfunction (SD). A consecutive series of 2379 patients was retrospectively studied. The analysis was focused on a subset of subjects (n = 1823; mean age 54.7 ± 11.4) selected for being free from overt prostatic diseases. Several parameters were investigated. After adjusting for confounders, the presence of an enlarged prostate size at DRE was associated with a higher risk of metabolic syndrome (HR = 1.346 (1.129-1.759); P = 0.030), type 2 diabetes mellitus (HR = 1.489 (1.120-1.980); P = 0.006), increased LDL cholesterol (>100 mg dl−1 ; HR = 1.354 (1.018-1.801); P = 0.037) and increased mean blood pressure (BP) values (HR = 1.017 (1.007-1.027) for each mmHg increment; P = 0.001). Accordingly, enlarged prostate size was also associated with a higher risk of arteriogenic erectile dysfunction (ED), as well as with other andrological conditions, such as varicocele and premature ejaculation (PE). PSA levels were significantly higher in subjects with enlarged prostate size when compared to the rest of the sample (HR = 3.318 (2.304; 4.799) for each log unit increment in PSA levels; P < 0.0001). Arteriogenic ED, according to different criteria, was also associated with increased PSA levels. In conclusion, our data support the need to examine prostate size either by clinical (DRE) or biochemical (PSA) inspection in subjects with SD, in order to have insights into the nature of the SD and the metabolic and cardiovascular (CV) background of the patient.