The analysis of retinal blood vessels present in fundus images, and the addressing of problems such as blood clot location, is important to undertake accurate and appropriate treatment of the vessels. Such tasks are hampered by the challenge of accurately tracing back problems along vessels to their source. This is due to the unresolved issue of distinguishing automatically between vessel bifurcations and vessel crossings in colour fundus photographs. In this paper, we present a new technique for addressing this problem using a convolutional neural network approach to firstly locate vessel bifurcations and crossings and then to classifying them as either bifurcations or crossings. Our method achieves high accuracies for junction detection and classification on the DRIVE dataset and we show further validation on an unseen dataset from which no data has been used for training. Combined with work in automated segmentation, this method has the potential to facilitate: reconstruction of vessel topography, classification of veins and arteries and automated localisation of blood clots and other disease symptoms leading to improved management of eye disease.