Abnormal vertical growth (AVG) causes significant yield losses to the Australian macadamia industry and the cause is unknown. Studies on the spread of AVG and molecular analysis of trees with AVG symptoms suggest the involvement of a slow spreading pathogen that does not produce copious amount of inoculum nor is spread by flying insects. The possibility that Bacillus megaterium, elements of a bipartite geminivirus and phytoplasmas are associated with AVG aetiology was investigated using specific PCR assays. Leaf samples from 118 trees including wild accessions of the four Macadamia species, and commercial cultivars of Hawaiian and Australian selections with and without AVG symptoms were tested. The assays detected geminiviral elements and B. megaterium, but not phytoplasma in trees with and without AVG symptoms. The absence of phytoplasmas together with no statistically significant relationship between the presence of either B. megaterium or geminiviral elements and AVG symptoms, suggests that all three agents are not the cause of the disease. The frequency of detection of B. megaterium was higher in samples from trees without AVG (66%) than trees with AVG (34%). In contrast, the frequency of detection of geminiviral elements was higher in trees with AVG (64%) than trees without AVG (36%). Geminiviral elements were detected in the wild accessions of the four Macadamia species, whereas B. megaterium was only detected in M. integrifolia and M. jansenii. The Hawaiian and Australian selections were positive for B. megaterium and geminiviral elements.