Filtered backprojection (FBP) is the traditional method for 13 N-NH 3 PET studies. Ordered-subsets expectation maximization (OSEM) is popular for PET studies because of better noise properties. Scant data exist on the effect of reconstruction algorithms on quantitative myocardial blood flow (MBF) estimation. Methods: Twenty patients underwent dynamic acquisition rest/stress 13 N-NH 3 studies. In Part 1, 19 rest/stress image pairs were reconstructed by FBP (10-mm Hanning filter) and by OSEM with 28 subsets and 2 (OSEM2), 6 (OSEM6), or 8 iterations (OSEM8), and a 10-mm postreconstruction smoothing gaussian filter. In Part 2, 9 image pairs were reconstructed by FBP (10-mm Hanning filter) and by OSEM with 28 subsets, 8 iterations, and a gaussian 5-, 10-, or 15-mm postreconstruction smoothing filter. Average MBF (mL/min/mL of myocardium) was calculated using a 3-compartment model. Results: Part 1: For rest MBF, the correlations between FBP and each of the OSEM algorithms were r 2 5 0.71, 0.73, and 0.77, respectively. MBF by OSEM6 (0.98 6 0.48 [mean 6 SD]) and OSEM8 (0.96 6 0.46) was not significantly different from FBP (1.02 6 0.39), but OSEM2 (0.80 6 0.37) was significantly lower (P , 0.0003). With stress, the correlations were high between FBP and OSEM6 and OSEM8 (r 2 5 0.85 and 0.90), and MBF by OSEM6 and OSEM8 was not significantly different from FBP. Part 2: Resting MBF correlated well between FBP and all OSEM smoothing filters (r 2 5 0.82, 0.85, and 0.88). Rest MBF using postsmoothing 5-or 10-mm filters was not different from FBP but was significantly lower with the 15-mm filter (P , 0.05). With stress, the correlations were good between FBP and OSEM regardless of smoothing (r 2 5 0.76, 0.77, and 0.79). However, MBF with postsmoothing 10-and 15-mm filters was significantly lower than by FBP (P , 0.05). Conclusion: Reconstruction algorithms significantly affect the estimation of quantitative blood flow data and should not be assumed to be interchangeable. Although aggressive smoothing may produce visually appealing images with reduced noise levels, it may cause an underestimation of absolute quantitative MBF. In selecting a reconstruction algorithm, an optimal balance between noise properties and diagnostic accuracy must be emphasized.