The outcome of Statistical Parametric Mapping (SPM) analyses of PET activation studies depends among others, on the quality of reconstructed data. In general, filtered back-projection (FBP) is used for reconstruction in PET activation studies. There is, however, increasing interest in iterative reconstruction algorithms such as ordered subset expectation maximization (OSEM) algorithms. The aim of the present study was to investigate the effects of reconstruction techniques and attenuation correction (AC) on the detection of activation foci following statistical analysis with SPM. First, a replicate study was performed to assess the effects of the reconstruction method on pixel variance. Second, a phantom study was performed to evaluate the influence of both locations of an activated area and applied reconstruction method on SPM outcome. A volumetric method was used to compute the number of false positive voxels for all reconstructions. In addition, average t values within activation foci and for false positive voxels were calculated. For the assessment of the effects of reconstruction on clinical data, a group of 11 patients was studied. For all reconstructions SPM maps were created and compared. Both the clinical and the phantom data showed that use of iterative reconstruction methods reduced false positive results, while showing similar SPM results within activated areas as FBP. Reconstruction of data without attenuation correction reduced noise for FBP only, but did not affect the quality of SPM results for OSEM. It is concluded that OSEM is a good alternative for FBP reconstructions providing SPM results with less noise.