A combination of manual physiotherapy and specific relaxation training effectively treats patients with chronic prostatitis/chronic pelvic pain syndrome. However, little information exists on myofascial trigger points and specific chronic pelvic pain symptoms. We documented relationships between trigger point sites and pain symptoms in men with chronic prostatitis/chronic pelvic pain syndrome. We randomly selected a cohort of 72 men who underwent treatment with physiotherapy and relaxation training from 2005 to 2008. Patients self-reported up to 7 pelvic pain sites before treatment and whether palpation of internal and external muscle trigger points reproduced the pain. Fisher's exact test was used to compare palpation responses, ie referral pain, stratified by reported pain site. Pain sensation at each anatomical site was reproduced by palpating at least 2 of 10 designated trigger points. Furthermore, 5 of 7 painful sites could be reproduced at least 50% of the time (p <0.05). The most prevalent pain sites were the penis in 90.3% of men, the perineum in 77.8% and the rectum in 70.8%. Puborectalis/pubococcygeus and rectus abdominis trigger points reproduced penile pain more than 75% of the time (p <0.01). External oblique muscle palpation elicited suprapubic, testicular and groin pain in at least 80% of the patients at the respective pain sites (p <0.01). This report shows relationships between myofascial trigger points and reported painful sites in men with chronic prostatitis/chronic pelvic pain syndrome. Identifying the site of clusters of trigger points inside and outside the pelvic floor may assist in understanding the role of muscles in this disorder and provide focused therapeutic approaches.