The aim was to determine if psychological factors favourably influence the short and long-term outcome of patients with sub-acute neck pain in terms of global perceived recovery, pain, using a Numerical Rating Scale (NRS) and functional disability, using the Neck Disability Index (NDI). This study was conducted within the framework of a randomised clinical trial comparing two types of conservative therapy in 146 patients with sub-acute neck pain. Multilevel techniques were used for data-analysis. The short and long term results for the three outcomes were very diverse. The sub-scales of the used questionnaires, i.e. the Pain Coping and Cognition List (PCCL), and the 4 Dimensional Symptom Questionnaire (4DSQ), did not contribute significantly to all of the multilevel models. Only the factor 'fear of movement' was consistently and significantly present in the univariable analysis for all outcomes at both follow-up measurements. The explained variance in the short term ranged from 16% to 30%, and from 6% to 34% in the long term. This can be considered to be low. We conclude that all psychological factors showed a considerable variation on the specific measurement and time point used. Only 'fear of movement' consistently impedes short term and long term recovery. Further prognostic research is needed to achieve more consistent results.