BACKGROUND: The safety of the manual treatment techniques such as spinal manipulation has been discussed and there is a need for more information about potential adverse events after manual therapy. The aim of this randomized controlled trial was to investigate differences in occurrence of adverse events between three different combinations of manual treatment techniques used by manual therapists (i.e. chiropractors, naprapaths, osteopaths, physicians and physiotherapists) for patients seeking care for back and/or neck pain. In addition women and men were compared regarding the occurrence of adverse events. METHODS: Participants were recruited among patients, ages 18-65, seeking care at the educational clinic of the Scandinavian College of Naprapathic Manual Medicine in Stockholm. The patients (n = 767) were randomized to one of three treatment arms 1) manual therapy (i.e. spinal manipulation, spinal mobilization, stretching and massage) (n = 249), 2) manual therapy excluding spinal manipulation (n = 258) and 3) manual therapy excluding stretching (n = 260). Treatments were provided by students in the seventh semester of total eight. Adverse events were measured with a questionnaire after each return visit and categorized in to five levels; 1) short minor, 2) long minor, 3) short moderate, 4) long moderate and 5) serious adverse events, based on the duration and/or severity of the event. Generalized estimating equations were used to examine the association between adverse event and treatments arms. RESULTS: The most common adverse events were soreness in muscles, increased pain and stiffness. No differences were found between the treatment arms concerning the occurrence of adverse event. Fifty-one percent of patients, who received at least three treatments, experienced at least one adverse event after one or more visits. Women more often had short moderate adverse events (OR = 2.19 (95% CI: 1.52-3.15)), and long moderate adverse events (OR = 2.49 (95% CI: 1.77-3.52)) compared to men. CONCLUSION: Adverse events after manual therapy are common and transient. Excluding spinal manipulation or stretching do not affect the occurrence of adverse events. The most common adverse event is soreness in the muscles. Women reports more adverse events than men. TRIAL REGISTRATION: This trial was registered in a public registry (Current Controlled Trials) (ISRCTN92249294).