To investigate the clinical and microbiological profiles from microbial keratitis following penetrating keratoplasty (PKP) in a tertiary referral center in Taiwan, the medical records of 648 consecutive patients (648 eyes) undergoing PKP between January 2003 and December 2007 were retrospectively reviewed. Patients who subsequently sustained microbial keratitis were enrolled and analyzed for potential risk factors, clinical manifestations, microbiological profiles, complications, graft survival, and final visual outcome. A total number of 42 corneal graft infections (6.5%) were recruited. Mean interval between corneal transplantation and graft infection was 12 ± 9.5 months. Potential risk factors included suture-related problems (31.0%), lid abnormalities (23.8%), persistent epithelial defect (23.8%), contact lens use (14.3%), dry eye (11.9%), and prior rejection episodes (4.8%). Lesions were discovered mostly at the donor-recipient junction ([DRJ] 45.2%). Positive cultures were identified in all of the morbid eyes, of which Pseudomonas aeruginosa was the most common pathogen (38.1%). Despite mandatory hospitalization and topical fortified antibiotics management, complications ensued such as graft failure (71.4%), hypopyon (21.4%), corneal perforation (14.3%), wound dehiscence (11.9%), and endophthalmitis (4.8%). The visual outcome was dismal that graft clarity was achieved in only 12 eyes (28.6%), and that final visual acuity deteriorated to less than 20/200 in 28 eyes (66.7%). In conclusion, microbial keratitis following PKP is a devastating event that severely impairs graft survival rate and postoperative visual outcome which usually occur within the first postoperative year. The incidence of post-PKP microbial keratitis has generally decreased in recent years whilst P. aeroginosa prevails as the leading cause of graft infection in our hospital. Close follow-up by ophthalmologists and elevated self-awareness of patients for at least one year are always encouraged to prevent late-onset infection.