The aim of this study is to assess the impact of objective (stretched) and subjective penile size in the erectile function in a urological check-up program on a cross-sectional study including 689 men aged 35–70 years. IIEF-5 questionnaire, physical examination (penile length, prostate volume, blood pressure, body mass index-BMI), metabolic syndrome (MS), comorbidities, habits (sexual intercourse frequency, physical activity, alcohol, and tobacco use), level of education, serum glucose, total testosterone, estradiol, PSA, lipid profile, and self-perceptions (ejaculation time and subjective penile size) were examined in multivariate models using logistic and linear regressions. Penile objective mean length was 13.08 cm ± 2.32 and 67 (9.72%) patients referred small penis self-perception. Seventy-six (11.03%) participants had severe erectile dysfunction (ED), 75 (10.88%) had mild to moderate and moderate ED, 112 (16.25%) had mild ED and 426 (61.83%) had no ED. Risk factors for ED that held statistical significance were self-perceived small penis (OR = 2.23, 95% CI 1.35–3.69, p = .0017), sexual intercourse frequency (per week) (OR = 0.45, 95% CI 0.38–0.52, p < .0001), satisfactory ejaculation time (no vs. yes, OR = 2.06, 95% CI 1.46–2.92, p < .0001), comorbidity (yes vs. no, OR = 2.01, 95% CI 1.46–2.76, p < .0001), age >65 years (OR = 2.93, 95% CI 1.53–5.61, p < .0001), tobacco use (yes vs. no, OR = 1.41, 95% CI 1.02–1.96, p < .0375), regular physical activity (no vs. yes, OR = 1.59, 95% CI 1.13–2.23, p < .0083), serum total testosterone < 200 ng/dl (OR = 3.48, 95% CI 1.69–7.16, p = 0.0009), serum glucose > 100 mg/dl (OR = 1.69, 95% CI 1.18–2.43, p = 0.0044) and systolic blood pressure > 130 mmHg (OR = 1.60, 95% CI 1.16–2.19, p = 0.0037). Results suggest that in addition to previously reported risk factors, patient’s subjective impressions of penile size negatively impacts sexual life in about 10% of men considered healthy, while objective penile length does not play significant role in erectile function.