Purpose: Whiplash trauma in motor vehicle accidents (MVA) may involve various painful soft tissue damages, but weeks/months later a minority of victims still suffers from various long-lasting and disabling symptoms, whiplash-associated disorders (WAD). The etiology is currently unknown, but X-ray-occult fractures may be one cause in some cases. The purpose of this prospective study was to examine the association between occult fractures, as seen on bone single photon emission computed tomography (SPECT), with neck-, head- and arm pain. Methods: An inception cohort of 107 patients presenting with acute whiplash symptoms following an MVA was invited to have a cervical SPECT shortly post injury and again 6 months later. Associations between occult fractures and pain levels at baseline, 6 and 12 months of follow-up were analyzed. Results: Eighty-eight patients had baseline SPECT performed at median 15 days (range 3-28) post injury, but only 49 patients accepted to have the follow-up SPECT at 6 months. Abnormal SPECT, defined as minimum one area of focal uptake, was seen in 32 patients at baseline, reflecting an occult fracture. Occult fractures were not associated with pain levels, neither at baseline nor at follow-up. Conclusion: Occult fractures do not seem to play a role for development of chronic pain after whiplash.