Although the settlement of deep foundations (piles, hereafter) is not generally a concern if the piles are driven to refusal, settlement can become a design issue if no stiff substratum is encountered. The settlement of individual and pairs of floating piles founded in a three-dimensional spatially random soil model are studied using finite element methods. A probabilistic model for total and differential settlement is developed and validated by Monte Carlo simulation. Moreover, this study investigates the reliability-based design factors required for the serviceability limit state design of deep foundations and recommends the geotechnical resistance and consequence factors required to achieve specified target reliability indices against excessive settlement of deep foundations. The effect of pile redundancy on geotechnical system design is also investigated.