The aim of this study is to obtain evidence supporting or negating the hypothesis that muscle pain is associated to sustained activation of low-threshold motor units. Long-term surface electromyographic (sEMG) recordings of trapezius activity pattern were related to subjectively reported shoulder and neck pain in work and leisure. Recordings from 118 female subjects (73 recorded both during work and leisure) were analyzed. Computer operators, secretaries, health care and retail workers were represented in the material. The recordings were calibrated by the root mean square (RMS)-detected response at maximal voluntary contraction (%EMG_max). The analysis was performed by quantifying duration and amplitude of sEMG activity exceeding 2% EMG_max ("EMG bursts"). Three response categories were defined by duration of the burst periods during work; low (<50%), intermediate (50-70%) and high (>70%) response groups. Shoulder and neck pain was assessed by hourly visual analogue score (VAS) throughout work and leisure and by pain score for the last 6 months. Shoulder and neck pain was higher at work than leisure for subjects with long-term pain in both the high and the low response groups. Persistent pain, defined by the 6-month score, was more prevalent in the high than the low and intermediate response groups (73% vs. 37%); relative risk 2.0. Trapezius activity was reduced from work to leisure for the high, but not the low response group. The activity pattern is consistent with low-threshold motor unit overexertion for the high, but not the low response group. We speculate that different mechanisms of muscle pain causation, dependent and independent of motor activity pattern, co-exist.