When projection data are incomplete for various technical reasons, artefacts may occur in the reconstructed images. This study examines whether an iterative reconstruction method, the ordered subsets implementation of the EM algorithm (OSEM), can improve reconstruction and minimise the artefacts compared to filtered back-projection (FBP). We varied the number and location of projections removed to investigate when significant artefacts occur, and whether diagnosis is affected. Phantom studies were analysed with sequential orthogonal pairs of projection angles removed (as would typically occur when either data loss or severe motion is detected during acquisition with a right-angled, dual-head cardiac single-photon emission tomography system) and reconstructed with both FBP and OSEM. Twelve normal myocardial perfusion studies were also assessed to study the effect of missing projections on clinical diagnosis. Differences between reconstructions with intact versus missing data were measured. Also, reconstructed images were clinically assessed and scored on a five-point scale based on whether the artefacts would alter clinical interpretation. Although both reconstruction methods showed artefacts, the absolute differences between reconstructed phantom data with intact and missing projection sets were significantly greater (P<0.005) for FBP than for OSEM for all numbers of missing projections. The clinical data showed similar differences between FBP and OSEM reconstructions. The three observers noted superiority of OSEM compared to FBP, with reduced incidence of clinically significant artefacts. However, neither reconstruction method could tolerate six or more missing pairs from 32 projections. There was no significant dependence on the angular location of missing projections. In the absence of any attempt to correct for missing projections, OSEM reduced the influence of artefacts compared to FBP.