They included abortion, gay rights and allowing gay men to give blood.
He has quit his job in the wake of his outspoken remarks linking those in gay relationships with child abuse.
It was a post that Mr Wells had coveted for many years.
His appointment to the job had come somewhat later than originally planned, as it is understood that the DUP was concerned about how Mr Wells, who was extremely outspoken on all of these issues, would deal with them as health minister.
In his first interview as the minister, I asked whether or not he would abandon his religious principles when making policy on issues like abortion and alcohol.
He asked for the interview to be stopped.
But after a brief stand-off and encouragement from his DUP aide and the health department's press officer, he agreed to continue and said he would not abandon his religious beliefs.
He spent his first day in the post blocking his critics on Twitter.
A short time in the post, Mr Wells managed to strike off a number of significant issues on his to-do list.
Perhaps his biggest achievement was ensuring an all-Ireland children's heart service will be up and running next month in Dublin.
Someone who made no secret of his views on smoking and drinking alcohol, he perhaps would say on a personal basis that his biggest achievement was introducing plain cigarette packaging and proposals for minimum pricing for alcohol.
Last month he announced that the meningitis B vaccine will be introduced in a child's routine vaccine programme, and that all hospitals will become smoke-free zones.
While not finalised, Mr Wells began the big conversation of reintroducing prescription charges in order to fund specialist drugs, especially for cancer.
A man who wore his heart on his sleeve, Mr Wells was always clear about his pro-life, anti-abortion views and also his feelings on gay rights.
Those issues remain unresolved in the in-tray and for his successor.
When Jim Wells came to the job of health minister, there was a range of contentious and extremely emotive issues waiting in his in-tray.