We present an approach MSIL-CRF that incorporates multiple instance learning (MIL) into conditional random fields (CRFs). It can generalize CRFs to work on training data with uncertain labels by the principle of MIL. In this work, it is applied to saving manual efforts on annotating training data for semantic segmentation. Specifically, we consider the setting in which the training dataset for semantic segmentation is a mixture of a few object segments and an abundant set of objects' bounding boxes. Our goal is to infer the unknown object segments enclosed by the bounding boxes so that they can serve as training data for semantic segmentation. To this end, we generate multiple segment hypotheses for each bounding box with the assumption that at least one hypothesis is close to the ground truth. By treating a bounding box as a bag with its segment hypotheses as structured instances, MSIL-CRF selects the most likely segment hypotheses by leveraging the knowledge derived from both the labeled and uncertain training data. The experimental results on the Pascal VOC segmentation task demonstrate that MSIL-CRF can provide effective alternatives to manually labeled segments for semantic segmentation.