The state of Johore, Malaysia had been hit by the worst flood in the Malaysian modern history on the 19th December 2006 (first wave) and the 12th January 2007 (second wave) affecting all the eight districts. A total number of 157,018 and 155,368 Johore population had been displaced by the first and the second wave event respectively. The Johore State Health Department activated the Flood Action Plan which include mobilising medical teams to conduct daily clinical examinations on the flood victims and health teams to inspect flood relief centres, food premises and homes at flood-hit areas with regard to prevent and control communicable diseases. The spreadsheet format was used to collect data on diseases, injury and death throughout the Johore flood disaster period starting from the 19th December 2006 until 19th February 2007. Analyses showed that 19,670 flood victims (36.3%) had communicable diseases and 34,530 (67.0%) had non-communicable diseases. As for the communicable diseases and symptoms/syndromes related to communicable disease, 41.3% were acute respiratory infections (ARI) followed by 25.9% skin infections, 19.1% fever, 10.1% acute gastroenteritis (AGE) and 3.0% acute conjunctivitis. Other infectious diseases include 61 notifiable diseases (46 food poisoning, 14 dengue fever and one tuberculosis), 20 leptospirosis (with two deaths), 20 chicken pox and two melioidosis cases. The Batu Pahat district had the highest incidence for the majority of the communicable diseases because of the prolonged flooding period. No cholera, typhoid, malaria, measles or hand-foot-mouth disease (HFMD) cases were detected among the Johore flood victims. Trends of disease incidence follow the number of evacuees placed in the relief centres corresponding to respective wave. A total of 507 flood victims had physical injuries related to flood mostly due to fall onto wet floor at the relief centres. Fifteen deaths due to drowning were mainly caused by accidental fall into the flood water. The incidence of communicable diseases encountered had been appropriately anticipated and managed attributed to enhanced public health control programmes augmented by syndromic and laboratory surveillance on potentialy fatal infectious diseases. Equal emphasis should be given to the surveillance and control of chronic diseases.