Spinal cord injury (SCI) produces damage to the somatic and autonomic pathways that regulate lower urinary tract, sexual, and bowel function, and increases the risk of autonomic dysreflexia. The recovery of these functions has a high impact on health, functioning, and quality of life and is set as the utmost priority by patients. The application of reliable models to predict lower urinary tract, sexual, and bowel function, and autonomic dysreflexia is important for guiding counseling, rehabilitation, and social reintegration. Moreover, a reliable prediction is essential for designing future clinical trials to optimize patients’ allocation to different treatment groups. To date, reliable and simple algorithms are available to predict lower urinary tract and bowel outcomes after traumatic and ischemic SCI. Previous studies identified a few risk factors to develop autonomic dysreflexia, albeit a model for prediction still lacks. On the other hand, there is an urgent need for a model to predict the evolution of sexual function. The aim of this review is to examine the available knowledge and models for the prediction of lower urinary tract, sexual, and bowel function, and autonomic dysreflexia after SCI, and critically discuss the research priorities in these fields.