An ordered subsets (OS) reconstruction algorithm based on the median root prior (MRP) and inter-update median filtering was implemented for the reconstruction of low count statistics transmission (TR) scans. The OS-MRP-TR algorithm was evaluated using an experimental phantom, simulating positron emission tomography (PET) whole-body (WB) studies, as well as patient data. Various experimental conditions, in terms of TR scan time (from 1 h to 1 min), covering a wide range of TR count statistics were evaluated. The performance of the algorithm was assessed by comparing the mean value of the attenuation coefficient (MVAC) of known tissue types and the coefficient of variation (CV) for low-count TR images, reconstructed with the OS-MRP-TR algorithm, with reference values obtained from high-count TR images reconstructed with a filtered back-projection (FBP) algorithm. The reconstructed OS-MRP-TR images were then used for attenuation correction of the corresponding emission (EM) data. EM images reconstructed with attenuation correction generated by OS-MRP-TR images, of low count statistics, were compared with the EM images corrected for attenuation using reference (high statistics) TR data. In all the experimental situations considered, the OS-MRP-TR algorithm showed: (1) a tendency towards a stable solution in terms of MVAC; (2) a difference in the MVAC of within 5% for a TR scan of 1 min reconstructed with the OS-MRP-TR and a TR scan of 1 h reconstructed with the FBP algorithm; (3) effectiveness in noise reduction, particularly for low count statistics data [using a specific parameter configuration the TR images reconstructed with OS-MRP-TR(1 min) had a lower CV than the corresponding TR images of a 1-h scan reconstructed with the FBP algorithm]; (4) a difference of within 3% between the mean counts in the EM images attenuation corrected using the OS-MRP-TR images of 1 min and the mean counts in the EM images attenuation corrected using the OS-MRP-TR images of 1 h; (5) preservation of "good" image quality for both TR and EM reconstructed images. In conclusion, the OS-MRP-TR algorithm is particularly suitable for WB PET studies, allowing: (1) the acquisition of a very short TR scan (within 1 min), (2) the reconstruction of such TR data in low-noise TR images and (3) the use of the reconstructed OS-MRP-TR images for attenuation correction of corresponding EM data.