Changes in vegetation cover, building construction, road network and traffic conditions caused by urban expansion affect the human habitat as well as the natural environment in rapidly developing cities. It is crucial to assess these changes and respond accordingly by identifying man-made and natural structures with accurate classification algorithms. With the increase in use of multi-sensor remote sensing systems, researchers are able to obtain a more complete description of the scene of interest. By utilizing multi-sensor data, the accuracy of classification algorithms can be improved. In this paper, we propose a method for combining 3D LiDAR point clouds and high-resolution color images to classify urban areas using Gaussian processes (GP). GP classification is a powerful non-parametric classification method that yields probabilistic classification results. It makes predictions in a way that addresses the uncertainty of real world. In this paper, we attempt to identify man-made and natural objects in urban areas including buildings, roads, trees, grass, water and vehicles. LiDAR features are derived from the 3D point clouds and the spatial and color features are extracted from RGB images. For classification, we use the Laplacian approximation for GP binary classification on the new combined feature space. The multiclass classification has been implemented by using one-vs-all binary classification strategy. The result of applying support vector machines (SVMs) and logistic regression (LR) classifier is also provided for comparison. Our experiments show a clear improvement of classification results by using the two sensors combined instead of each sensor separately. Also we found the advantage of applying GP approach to handle the uncertainty in classification result without compromising accuracy compared to SVM, which is considered as the state-of-the-art classification method.