BACKGROUND: Among the working population, non-specific low-back pain and neck pain are one of the most common reasons for sickness absenteeism. The aim was to evaluate the effects of an early intervention of yoga - compared with strength training or evidence-based advice - on sickness absenteeism, sickness presenteeism, back and neck pain and disability among a working population. METHODS: A randomized controlled trial was conducted on 159 participants with predominantly (90%) chronic back and neck pain. After screening, the participants were randomized to kundalini yoga, strength training or evidence-based advice. Primary outcome was sickness absenteeism. Secondary outcomes were sickness presenteeism, back and neck pain and disability. Self-reported questionnaires and SMS text messages were completed at baseline, 6 weeks, 6 and 12 months. RESULTS: The results did not indicate that kundalini yoga and strength training had any statistically significant effects on the primary outcome compared with evidence-based advice. An interaction effect was found between adherence to recommendations and sickness absenteeism, indicating larger significant effects among the adherers to kundalini yoga versus evidence-based advice: RR = 0.47 (CI 0.30; 0.74, p = 0.001), strength training versus evidence-based advice: RR = 0.60 (CI 0.38; 0.96, p = 0.032). Some significant differences were also found for the secondary outcomes to the advantage of kundalini yoga and strength training. CONCLUSIONS: Guided exercise in the forms of kundalini yoga or strength training does not reduce sickness absenteeism more than evidence-based advice alone. However, secondary analyses reveal that among those who pursue kundalini yoga or strength training at least two times a week, a significantly reduction in sickness absenteeism was found. Methods to increase adherence to treatment recommendations should be further developed and applied in exercise interventions. TRIAL REGISTRATION: Clinicaltrials.gov NCT01653782, date of registration: June, 28, 2012, retrospectively registered.