In 2007, Mrs McCann was subject to a harrowing interview by Portuguese police which asked her such questions as, "Why did you say Madeleine had been abducted?"
The couple have been cleared of any wrongdoing and British and Portuguese police have insisted they are no longer suspects.
The McCanns travelled to the Algarve in April 2007 with Madeleine, her brother Sean, sister Amelie, and a group of friends. Madeleine disappeared five days later.
The documentary looks at theories about the case, including the idea that she was snatched to order by a people-trafficking gang and smuggled to another country.
At the time of the disappearance, Portuguese police asked Kate McCann what she meant when she said in reference to her daughter, "We let her down".
She was also quizzed about getting the media involved.
The barrage of queries led ultimately to the question: "Did you have any responsibility or intervention in your daughter's disappearance?"
The 48 questions Kate McCann did not answer
1. On May 3, 2007, around 22:00, when you entered the apartment, what did you see? What did you do? Where did you look? What did you touch?
2. Did you search inside the master bedroom wardrobe?
3. (Shown two photographs of her bedroom wardrobe) Can you describe its contents?
4. Why was the curtain by the sofa near the side window tampered with? Did someone go behind the sofa?
5. How long did your search of the apartment take after you detected Madeleine's disappearance?
6. Why did you say Madeleine had been abducted?
7. Assuming Madeleine was abducted, why did you leave the twins to go to the 'Tapas' and raise the alarm? The supposed abductor could still be in the apartment.
8. Why didn't you ask the twins then what happened to their sister or why didn't you ask them later on?
9. When you raised the alarm at the 'Tapas' what exactly did you say – what were your exact words?
10. What happened after you raised the alarm there?
11. Why did you go and warn your friends instead of shouting from the veranda?
12. Who contacted the authorities?
13. Who took place in the searches?
14. Did anyone outside the group learn of her disappearance in those following minutes?
15. Did any neighbour offer you help?
16. What does 'we let her down' mean?
17. Did Jane Tanner tell you that night she'd seen a man with a child?
18. How were the authorities contacted and which police force was alerted?
19. During the searches, with the police there, where did you search for Maddie, how and in what way?
20. Why did the twins not wake up during that search or when they were taken upstairs?
21. Who did you phone after the occurrence?
22. Did you call Sky News?
23. Did you know the danger of calling the media, because it could influence the abductor?
24. Did you ask for a priest?
25. By what means did you divulge Madeleine's features, by photographs or by any other means?
26. Is it true that during the searches you remained seated on Maddie's bed without moving?
27 What was your behaviour that night?
28. Did you manage to sleep?
29. Before travelling to Portugal, did you make any comment about a foreboding or a bad feeling?
30. What was Madeleine's behaviour like?
31. Did Maddie suffer from any illness or take any medication?
32. What was Madeleine's relationship like with her brother and sister?
33. What was Madeleine's relationship like with her brother and sister, friends and school mates?
34. As for your professional life, in how many and which hospitals have you worked?
35. What is your medical speciality?
36. Have you ever done shift work in any emergency services or other services?
37. Did you work every day?
38. At a certain point you stopped working. Why?
39. Are the twins difficult to get to sleep? Are they restless and does that cause you uneasiness?
40. Is it true sometimes you despaired at your children's behaviour and it left you feeling very uneasy?
41. Is it true that in England you even considered handing over Madeleine's custody to a relative?
42. In England, did you medicate your children? What type of medication?
43. In the case files, you were shown canine forensic testing films. After watching them, did you say you couldn't explain any more than you already had?
44. When the sniffer dog also marked human blood behind the sofa, did you say you couldn't explain any more than you already had?
45. When the sniffer dog marked the scent of corpse coming from the vehicle you hired a month after the disappearance, did you say you couldn't explain any more than you already had?
46. When human blood was marked in the boot of the vehicle, did you say you couldn't explain any more than you already had?
47. When confronted with the results of Maddie's DNA, carried out in a British lab, collected from behind the sofa and the boot of the vehicle, did you say you couldn't explain any more than you already had?
48. Did you have any responsibility or intervention in your daughter's disappearance?