To describe and analyze subjective and objective scintigraphic findings in horses with paranasal sinus disorders. Horses with suspected disorders of the paranasal sinuses or cheek teeth (n = 48) and control horses (n = 30). 99Technetium-methylenediphosphate (99Tc-MDP; 7500 MBq) was administered for scintigraphic examination of the skull. Abnormal patterns of increased radionuclide uptake (IRU) were identified and subjectively described. Scintigrams and radiographs were blindly assessed by 2 clinicians and the accuracy of the imaging modalities was compared. Objective analysis was performed by comparing regions of interest (ROI) drawn over areas of abnormal IRU to the equivalent area on the unaffected side using the Mann-Whitney test. An ROI ratio (affected:non-affected sides) was also calculated for each lesion. Twenty-eight horses were diagnosed with primary (15) or secondary (13) sinusitis. Nine primary sinusitis cases had focal area(s) of moderate or marked IRU in addition to a more diffuse uptake in the affected sinus(es). kappa was marginally higher for scintigraphic assessment of paranasal sinus disorders than for radiographic assessment. There were significant differences in mean counts/pixel in ROI drawn on the affected side compared with the non-affected side. There was considerable overlap between the magnitudes of ROI ratios found with many different disorders. Scintigraphy can be useful for differentiation of sinusitis of dental origin from other causes of sinusitis. Quantitative analysis of scintigrams is not reliable for identification of particular disorders. Focal areas of moderate or marked IRU may be observed with primary sinusitis. Careful 3-dimensional localization of the lesion, along with consideration of other clinical and diagnostic findings should be performed to prevent false-positive diagnoses of periapical infection in such instances.