Neutron coincidence and multiplicity counting is a standard technique used to measure uranium and plutonium masses in unknown samples for nuclear safeguards purposes, but background sources of radiation can obscure the results. In particular, high energy cosmic rays can produce large coincidence count contributions. Since some of the events occur in the sample itself, it is impossible to measure the background separately. This effect greatly increases the limit of detection of some low level neutron coincidence counting applications.The cosmic ray capability of MCNP6 was used to calculate the expected coincidence rates from cosmic rays for different sample configurations and experimental measurements were conducted for comparison. Uranium enriched to 66%, lead bricks, and an empty detector were measured in the mini Epithermal Neutron Multiplicity Counter, and MCNP6 simulations were made of the same measurements. The results show that the capability is adequate for predicting the expected background rates.Additional verification of MCNP6 was given by comparison of particle production rates to other publications, increasing confidence in MCNP6׳s use as a tool to lower the limit of detection. MCNP6 was then used to find particle and source information that would be difficult to detect experimentally. The coincidence count contribution was broken down by particle type for singles, doubles, and triples rates. The coincidence count contribution was broken down by source, from(a,n), spontaneous fission, and cosmic rays, for each multiplicity.