Pinhole SPECT is rapidly gaining popularity for imaging laboratory animals using gamma-emitting molecules. Penetration and scattering of gamma radiation in the pinhole edge material can account for a significant fraction of the total number of photons detected, particularly if the pinholes have small diameters. This study characterizes the effects of penetration and scatter with micro-pinholes made of lead, tungsten, gold and platinum. Monte Carlo simulations are performed for I-125 (27-35 keV) and Tc-99m (140 keV) point sources with pinhole diameters ranging from 50 to 500 mum. The simulations account for the effects of photo-electric interaction, Rayleigh scattering, Compton scattering, ionization, bremsstrahlung and electron multiple scattering. As a typical example, in the case of a Tc-99m point source and pinholes with a diameter of 300 mum in gold or platinum, approximately 55% of the photons detected resulted from penetration and approximately 3% from scatter. For pinhole diameters ranging from 100 to 500 mum, the penetration fraction for tungsten and lead was approx a factor of 1.0 to 1.6 higher and the scatter fraction was 1.0 to 1.8 times higher than in case of gold or platinum. Using I-125 instead of Tc-99m decreases the penetration fraction by a factor ranging from 3 to 11 and the scatter fraction by a factor ranging from 12 to 40. For all materials studied, the total amounts of penetrated and scattered photons changed approximately linearly with respect to the pinhole diameter.