BACKGROUND: Determination of the mode of action of new exercise techniques in different back pain populations is lacking. The effectiveness of supplementing an exercise programme with stabilisation exercises concerning physiological and functional parameters in non-specific back pain patients is unknown. METHODS: Randomised controlled trial, comparing a general trunk muscle endurance exercise approach enhanced with specific muscle stabilisation exercises (S&G group) with a general exercise approach only (G group). 55 patients with recurrent back pain were randomised in S&G group (n=29) and G group (n=26). Both groups received an 8-week exercise intervention and written advice. Paraspinal muscle strength and electromyographic fatigue of the erector spinae and multifidus were measured. Additionally, 3 functional speed tests were assessed. Outcomes were collected pre- and post-intervention. FINDINGS: No differences were detected for any of the paraspinal fatigue characteristics either within or between groups, apart from a significant decrease in normalised median frequency slope of the erector spinae for the G group. Paraspinal muscle strength and all functional tests have demonstrated significant within-group improvements for both groups, without any between-group differences. INTERPRETATION: An 8-week stabilisation exercise-enhanced approach presented equal benefits to a general endurance-based exercise programme for patients with recurrent non-specific back pain. A slightly steeper slope for the erector spinae in the G group was the only electromyographic fatigue alteration noted. Concomitant strength improvement probably reflects neural input changes rather than histochemical muscle changes. Physical exercise alone and not the exercise type was the key determinant for improvement in this patient group.