This work deals with a methodology to assess the influence of the spherical clearance joints in spatial multibody systems. The methodology is based on the Cartesian coordinates, with the dynamics of the joint elements modeled as impacting bodies and controlled by contact forces. The impacts and contacts are described by a continuous contact force model that accounts for geometric and mechanical characteristics of the contacting surfaces. The contact force is evaluated as function of the elastic pseudo-penetration between the impacting bodies, coupled with a nonlinear viscous-elastic factor representing the energy dissipation during the impact process. A spatial four-bar mechanism is used as an illustrative example and some numerical results are presented, with the efficiency of the developed methodology discussed in the process of their presentation. The results obtained show that the inclusion of clearance joints in the modelization of spatial multibody systems significantly influences the prediction of components’ position and drastically increases the peaks in acceleration and reaction moments at the joints. Moreover, the system’s response clearly tends to be nonperiodic when a clearance joint is included in the simulation.