The postoperative effect on penile length after radical prostatectomy has been the subject of studies with conflicting results. We analyzed self-perceived penile shortening, quality of life and self-esteem after radical prostatectomy. In this cross-sectional study of a cohort of 1411 men who underwent a radical prostatectomy at Karolinska University Hospital between 2002 and 2006, we used a study-specific questionnaire. Patients and controls were asked about their perceived penile shortening by comparing present penile length now and at age 30 years. All subjects were also asked about their present quality of life and self-esteem. Patients were compared with 442 age-matched population-based controls. Among 1288 who underwent radical prostatectomy and answered the questionnaire (response rate 91%), 663 patients reported self-perceived penile shortening (55%), as compared with 85 (26%) of 350 men in the control group, corresponding to a relative risk (RR) of 2.1 (95% confidence interval (CI) 1.8-2.6) of self-perceived penile shortening compared with the age-matched control group. Age, grade of erectile dysfunction and angina were correlated with self-perceived penile shortening in both the operated and the control group. After adjustments for all of these mentioned potential confounders, we obtained a RR of 1.7 (95% CI 1.4-2.1) of self-perceived penile shortening compared with the controls. We also found that self-assessed penile shortening was associated with a RR of 1.2 (95% CI 1.1-1.3) for a low-to-moderate self-assessed quality of life and a RR of 1.2 (95% CI 1.1-1.4) for a low-to-moderate self estimation of self-esteem. Extensive nerve-sparing technique seems to be associated with less self-perceived penile shortening compared with radical prostatectomy with lower degree of nerve-sparing approach. These data indicate that radical prostatectomy is associated with self-perceived penile shortening and suggests that erectile function is a key factor in penile shortening.