Objectives: Few studies have measured the long-term effects of computerised provider order entry systems on pathology test turnaround time. Further, a recent study has raised the possibility that such systems, which require significant work practice change, may be associated with an increase in mortality rates. Our study answered two questions in relation to system introduction in a major Australian teaching hospital: i) are improvements in turnaround times achieved in the first 12 months after system introduction sustained 24 months post-implementation; and ii) do mortality rates change following the introduction of an order entry system? Methods: Turnaround time and mortality rates 5 months before and 12 and 24 months after implementation of a computerised order entry system were measured. Turnaround time was defined as the time from receipt of a specimen and order in a laboratory to availability of a result. Results: Improvements in turnaround time achieved in the first 12 months were sustained with a further significant 12.6% reduction at 24 months post-implementation, with no change in average number of tests per patient. The mortality rate significantly increased in the year following system introduction but returned to the pre-system rate in the second year of system use. Review of the excess deaths demonstrated these were most likely attributable to a coincidental influenza outbreak and not to system introduction. Conclusions: The computerised provider order entry system produced sustained and continuing improvements in laboratory efficiency over a two-year period. Associations between increased mortality rates and system introduction should be investigated carefully to ascertain any likely association.