In the aftermath of the unprecedented flooding in 2010 that devastated large areas of the country and directly affected over 20 million people, the incidence of water, sanitation and hygiene related diseases, including acute diarrhea, among the affected population was a major concern. In Pakistan, diarrhoea is the leading cause of mortality for children under 5 with 116,000 children perishing each year. The gap between the real progress and the MDG target for sanitation increased because floods washed away the gains made in the sanitation sector in rural areas. This paper presents the practical experience of developing and implementing a new rural sanitation programme in a post-flood situation with the objective to scale up the Pakistan Approach to Total Sanitation and to reach out to an estimated 7.6 million flood-affected people in 34 districts of Pakistan to safeguard and protect their health from water-borne diseases. The programme uses “triggering” as an entry point and puts a larger focus on behavioral change for sanitation and hygiene. The Program takes into account the integrated total sanitation model seeking to undertake a series of measures aiming at ensuring raising awareness through appropriate means of communication, attaining and sustaining an open defecation free status, promoting the use of secondary barriers and 100 % safe management of excreta through end of pipe treatment options. The programme was conceived on the premise that a market for sanitation goods and services must be operative to meet the increase demand for sanitation improvements resulting from behavioral change campaign.