Congenitally absent or hypoplastic L5-S1 facet (zygapophyseal) joints are an aberrated rarity, with less than 30 reported cases. This absence of facet joint and contralateral hypertrophic facet provides a continuum of presentations that can complicate low back pain (LBP) diagnoses and management. A broad differential including lumbar facet syndrome, disc degeneration, spinal stenosis, herniated radiculopathy, spondyloarthropathies and sacroiliac joint pain should be considered initially, with the flexibility for other diagnoses. Understanding the effects of different anatomical, biomechanical and physiological changes on spinal health is essential for patient care. We report a progression of lumbar radiculopathy complicated by the presence of a congenitally absent left L5-S1 facet joint and hypertrophic right L5-S1 facet joint. Furthermore, our discussion concentrates on pathophysiology, differential diagnoses and management of congenitally absent facet joints and the impact they can have on LBP and spinal health.